The David H. Koch Institute for Integrative Cancer Research at MITThe David H. Koch Institute for Integrative Cancer Research at MIT

Massachusetts Institute of Technology

National Cancer Institute Cancer Center

Science + Engineering... Conquering Cancer Together

Progress: April 2016

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1. Machine Life. Lu TK, Purcell O. Sci Am. pubmed:27082194;  doi:10.1038/scientificamerican0416-58

2. Parallel in-vivo assessment of drug phenotypes at various time points during systemic BRAF inhibition reveals tumor adaptation and altered treatment vulnerabilities. Jonas O, Oudin MJ, Kosciuk T, Whitman M, Gertler FB, Cima MJ, Flaherty KT, Langer R. Clin Cancer Res. pubmed:27091406;  doi:10.1158/1078-0432.CCR-15-2722

3. A Subset of Latency-Reversing Agents Expose HIV-Infected Resting CD4+ T-Cells to Recognition by Cytotoxic T-Lymphocytes. Jones RB, Mueller S, O'Connor R, Rimpel K, Sloan DD, Karel D, Wong HC, Jeng EK, Thomas AS, Whitney JB, Lim SY, Kovacs C, Benko E, Karandish S, Huang SH, Buzon MJ, Lichterfeld M, Irrinki A, Murry JP, Tsai A, Yu H, Geleziunas R, Trocha A, Ostrowski MA, Irvine DJ, Walker BD. PLoS Pathog. pubmed:27082643;  doi:10.1371/journal.ppat.1005545

4. The Mbd4 DNA glycosylase protects mice from inflammation-driven colon cancer and tissue injury. Yu AM, Calvo JA, Muthupalani S, Samson LD. Oncotarget. pubmed:27086921;  doi:10.18632/oncotarget.8721

5. A Thermodynamic Based Interpretation of Protein Expression Heterogeneity in Different GBM Tumors Identifies Tumor Specific Unbalanced Processes. Kravchenko-Balasha N, Johnson H, White FM, Heath JR, Levine RD. J Phys Chem B. pubmed:27035264;  doi:10.1021/acs.jpcb.6b01692

6. Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance. Miller MA, Oudin MJ, Sullivan RJ, Wang SJ, Meyer AS, Im H, Frederick DT, Tadros J, Griffith LG, Lee H, Weissleder R, Flaherty KT, Gertler FB, Lauffenburger DA. Cancer Discov. pubmed:26984351;  doi:10.1158/2159-8290.CD-15-0933

7. Designer Dual Therapy Nanolayered Implant Coatings Eradicate Biofilms and Accelerate Bone Tissue Repair. Min J, Choi KY, Dreaden EC, Padera RF, Braatz RD, Spector M, Hammond PT. ACS Nano. pubmed:26923427;  doi:10.1021/acsnano.6b00087

8. Seeing through the interface: poly(epsilon-Caprolactone) surface modification of poly(glycerol-co-sebacic acid) membranes in adult porcine retinal explants. Taylor L, Arner K, Kolewe M, Pritchard C, Hendy G, Langer R, Ghosh F. J Tissue Eng Regen Med. pubmed:27098673;  doi:10.1002/term.2135

9. Poly(Limonene Thioether) Scaffold for Tissue Engineering. Fischer KM, Morgan KY, Hearon K, Sklaviadis D, Tochka ZL, Fenton OS, Anderson DG, Langer R, Freed LE. Adv Healthc Mater. pubmed:26890480;  doi:10.1002/adhm.201500892

10. Bioinspired Alkenyl Amino Alcohol Ionizable Lipid Materials for Highly Potent In Vivo mRNA Delivery. Fenton OS, Kauffman KJ, McClellan RL, Appel EA, Dorkin JR, Tibbitt MW, Heartlein MW, DeRosa F, Langer R, Anderson DG. Adv Mater. pubmed:26889757;  doi:10.1002/adma.201505822

11. Control of liver size by RNAi-mediated multiplex knockdown and its application for discovery of regulatory mechanisms. Yin H, Bogorad RL, Barnes C, Walsh S, Zhuang I, Nonaka H, Ruda V, Kuchimanchi S, Nechev L, Akinc A, Xue W, Zerial M, Langer R, Anderson DG, Koteliansky V. J Hepatol. pubmed:26658687;  doi:10.1016/j.jhep.2015.11.028

12. Sustained Local Release of Methylprednisolone from a Thiol-Acrylate Poly(Ethylene Glycol) Hydrogel for Treating Chronic Compressive Radicular Pain. Slotkin JR, Ness JK, Snyder KM, Skiles AA, Woodard EJ, O'Shea T, Layer RT, Aimetti AA, Toms SA, Langer R, Tapinos N. Spine (Phila Pa 1976). pubmed:26630427;  doi:10.1097/BRS.0000000000001309

13. PD-1 marks dysfunctional regulatory T cells in malignant gliomas. Lowther DE, Goods BA, Lucca LE, Lerner BA, Raddassi K, van Dijk D, Hernandez AL, Duan X, Gunel M, Coric V, Krishnaswamy S, Love JC, Hafler DA. JCI Insight. pubmed:27182555;  doi:10.1172/jci.insight.85935

14. Inhibition of Zinc-Dependent Histone Deacetylases with a Chemically Triggered Electrophile. Boskovic ZV, Kemp MM, Freedy AM, Viswanathan VS, Pop MS, Fuller JH, Martinez NM, Figueroa Lazu SO, Hong JA, Lewis TA, Calarese D, Love JD, Vetere A, Almo SC, Schreiber SL, Koehler AN. ACS Chem Biol. pubmed:27064299;  doi:10.1021/acschembio.6b00012

15. Flexible Octopus-Shaped Hydrogel Particles for Specific Cell Capture. Chen L, An HZ, Haghgooie R, Shank AT, Martel JM, Toner M, Doyle PS. Small. pubmed:26929053;  doi:10.1002/smll.201600163

16. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Tirosh I, Izar B, Prakadan SM, Wadsworth MH2nd, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin JR, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CG, Kazer SW, Gaillard A, Kolb KE, Villani AC, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jane-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA. Science. pubmed:27124452;  doi:10.1126/science.aad0501

17. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Conway AE, Van Nostrand EL, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, Freese P, Lambert NJ, Sathe S, Liang TY, Essex A, Landais S, Burge CB, Jones DL, Yeo GW. Cell Rep. pubmed:27068461;  doi:10.1016/j.celrep.2016.03.052

18. Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Giannakis M, Mu XJ, Shukla SA, Qian ZR, Cohen O, Nishihara R, Bahl S, Cao Y, Amin-Mansour A, Yamauchi M, Sukawa Y, Stewart C, Rosenberg M, Mima K, Inamura K, Nosho K, Nowak JA, Lawrence MS, Giovannucci EL, Chan AT, Ng K, Meyerhardt JA, Van Allen EM, Getz G, Gabriel SB, Lander ES, Wu CJ, Fuchs CS, Ogino S, Garraway LA. Cell Rep. pubmed:27149842;  doi:10.1016/j.celrep.2016.03.075

19. Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Tan JL, Fogley RD, Flynn RA, Ablain J, Yang S, Saint-Andre V, Fan ZP, Do BT, Laga AC, Fujinaga K, Santoriello C, Greer CB, Kim YJ, Clohessy JG, Bothmer A, Pandell N, Avagyan S, Brogie JE, van Rooijen E, Hagedorn EJ, Shyh-Chang N, White RM, Price DH, Pandolfi PP, Peterlin BM, Zhou Y, Kim TH, Asara JM, Chang HY, Young RA, Zon LI. Mol Cell. pubmed:27058786;  doi:10.1016/j.molcel.2016.03.013

20. Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML. Puram RV, Kowalczyk MS, de Boer CG, Schneider RK, Miller PG, McConkey M, Tothova Z, Tejero H, Heckl D, Jaras M, Chen MC, Li H, Tamayo A, Cowley GS, Rozenblatt-Rosen O, Al-Shahrour F, Regev A, Ebert BL. Cell. pubmed:27058663;  doi:10.1016/j.cell.2016.03.015

21. Transcriptome-scale RNase-footprinting of RNA-protein complexes. Ji Z, Song R, Huang H, Regev A, Struhl K. Nat Biotechnol. pubmed:26900662;  doi:10.1038/nbt.3441

22. Chromosome-Specific and Global Effects of Aneuploidy in Saccharomyces cerevisiae. Dodgson SE, Kim S, Costanzo M, Baryshnikova A, Morse DL, Kaiser CA, Boone C, Amon A. Genetics. pubmed:26837754;  doi:10.1534/genetics.115.185660

23. The Conserved VPS-50 Protein Functions in Dense-Core Vesicle Maturation and Acidification and Controls Animal Behavior. Paquin N, Murata Y, Froehlich A, Omura DT, Ailion M, Pender CL, Constantine-Paton M, Horvitz HR. Curr Biol. pubmed:26948874;  doi:10.1016/j.cub.2016.01.049

24. Treatment response assessment in IDH-mutant glioma patients by non-invasive 3D functional Spectroscopic Mapping of 2-Hydroxyglutarate. Andronesi OC, Loebel F, Bogner W, Marjanska M, Vander Heiden MG, Iafrate AJ, Dietrich J, Batchelor T, Gerstner ER, Kaelin WJr, Chi AS, Rosen B, Cahill DP. Clin Cancer Res. pubmed:26534967;  doi:10.1158/1078-0432.CCR-15-0656

25. High fat diet and stem cells: Linking diet to intestinal tumor formation. Cangelosi AL, Yilmaz OH. Cell Cycle. pubmed:27097128;  doi:10.1080/15384101.2016.1175275

26. A requirement for filopodia extension toward Slit during Robo-mediated axon repulsion. McConnell RE, Edward van Veen J, Vidaki M, Kwiatkowski AV, Meyer AS, Gertler FB. J Cell Biol. pubmed:27091449;  doi:10.1083/jcb.201509062

27. Tobacco mosaic virus delivery of phenanthriplatin for cancer therapy. Czapar AE, Zheng YR, Riddell IA, Shukla S, Awuah SG, Lippard SJ, Steinmetz NF. ACS Nano. pubmed:26982250;  doi:10.1021/acsnano.5b07360

28. Interaction between the Rev1 C-Terminal Domain and the PolD3 Subunit of Polzeta Suggests a Mechanism of Polymerase Exchange upon Rev1/Polzeta-Dependent Translesion Synthesis. Pustovalova Y, Magalhaes MT, D'Souza S, Rizzo AA, Korza G, Walker GC, Korzhnev DM. Biochemistry. pubmed:26982350;  doi:10.1021/acs.biochem.5b01282

29. Kicking Genomic Profiling to the Curb: How Re-wiring the Phosphoproteome Can Explain Treatment Resistance in Glioma. Lam FC, Yaffe MB. Cancer Cell. pubmed:27070697;  doi:10.1016/j.ccell.2016.03.022